I seem to be experiencing this almost all the time on my engineers with turrets not spawning even though I'm in the animation to place them for extended periods of time.
My drone has the same problem.
And I've also gone through the beam weapon firing animations (full auto assault weapons usually) with nothing happening except some weird longer than normal cooldown on regular attacks.
I've even occasionally gotten some secondary global cooldown on the full auto spread attack.
I get especially a lot with torpedoes... as well as when I try to activate several abilities one after the other very quickly.
I'll get a global cooldown and even the effect of the ability in question for about a second, but it wont actually activate (the graphical effect will stop, and it's own cooldown wont trigger).. so i have to hit the corresponding button again.
Sometimes I find when I try to click on an ability from the BO tray nothing happens until I click a couple of times on some other graphic like space or another ship and then reclick the ability icon. I was wondering if it had anything to do with playing in windowed mode and if it's related to the game getting stuck on mouse look as well.
I experience random power effects with powers I do not posses at times when I chain several powers together for effect. In one game I hit BFI+AUxSIF+GDF and got the added bonus of CPB going off as well, expect I didn't have CPB on that build.
Sometimes the cooldown timer engages, but not the ability.
I have experienced this with Torpedo: High Yield. It seems that there is a short time window (couple of tenths of a second) after the ability finishes recharging when clicking the icon causes the cooldown to start again without activating the ability. It's really annoying.